1.1_clean_adata.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook is to clean adata, add the counts in the same barcode"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "import scanpy as sc\n",
    "import os\n",
    "import re\n",
    "import scipy as scp\n",
    "import pandas as pd\n",
    "import scvelo as scv\n",
    "import anndata as ad"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 223413 × 22555 \n",
       "    obs: 'folder', 'n_genes'\n",
       "    var: 'n_cells'\n",
       "    layers: 'spliced', 'unspliced'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = sc.read_h5ad('processed_adata.h5ad')\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>treatment</th>\n",
       "      <th>replicate</th>\n",
       "      <th>barcodes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SCC1</td>\n",
       "      <td>CTX</td>\n",
       "      <td>R1</td>\n",
       "      <td>AAACCTGAGTTGTCGT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SCC1</td>\n",
       "      <td>CTX</td>\n",
       "      <td>R1</td>\n",
       "      <td>AAACCTGCACAGCGTC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SCC1</td>\n",
       "      <td>CTX</td>\n",
       "      <td>R1</td>\n",
       "      <td>AAACCTGGTACTTCTT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SCC1</td>\n",
       "      <td>CTX</td>\n",
       "      <td>R1</td>\n",
       "      <td>AAAGATGGTGTGAATA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SCC1</td>\n",
       "      <td>CTX</td>\n",
       "      <td>R1</td>\n",
       "      <td>AAAGCAAGTAGCTGCC</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   cell treatment replicate          barcodes\n",
       "0  SCC1       CTX        R1  AAACCTGAGTTGTCGT\n",
       "1  SCC1       CTX        R1  AAACCTGCACAGCGTC\n",
       "2  SCC1       CTX        R1  AAACCTGGTACTTCTT\n",
       "3  SCC1       CTX        R1  AAAGATGGTGTGAATA\n",
       "4  SCC1       CTX        R1  AAAGCAAGTAGCTGCC"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "phenoDat = pd.read_csv('phenoSCCall.csv')\n",
    "phenoDat.drop('Unnamed: 0',axis=1, inplace=True)\n",
    "phenoDat.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Clean the adata to add counts from same cell "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
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       "      <th>ENSG00000001460.18</th>\n",
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       "      <th>ENSG00000237126.8</th>\n",
       "      <th>ENSG00000236699.9</th>\n",
       "      <th>ENSG00000242252.2</th>\n",
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       "      <th>AAACCTGAGCGATTCT-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 22555 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "index               ENSG00000001460.18  ENSG00000001461.17  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000010072.16  ENSG00000009780.15  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000048707.15  ENSG00000059588.10  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 1.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000041988.15  ENSG00000049245.13  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 2.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000052723.11  ENSG00000058799.15        ...          \\\n",
       "index                                                             ...           \n",
       "AAACCTGAGCGATTCT-0                 1.0                 0.0        ...           \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0        ...           \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0        ...           \n",
       "\n",
       "index               ENSG00000161835.11  ENSG00000173809.18  ENSG00000237126.8  \\\n",
       "index                                                                           \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0                0.0   \n",
       "\n",
       "index               ENSG00000236699.9  ENSG00000242252.2  ENSG00000242461.1  \\\n",
       "index                                                                         \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                0.0   \n",
       "\n",
       "index               ENSG00000231364.3  ENSG00000288023.1  ENSG00000211445.12  \\\n",
       "index                                                                          \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                 0.0   \n",
       "\n",
       "index               ENSG00000267547.1  \n",
       "index                                  \n",
       "AAACCTGAGCGATTCT-0                0.0  \n",
       "AAACCTGAGCTTTGGT-0                0.0  \n",
       "AAACCTGAGGCCCTCA-0                0.0  \n",
       "AAACCTGAGTAGCCGA-0                0.0  \n",
       "AAACCTGGTAGCGCTC-0                0.0  \n",
       "\n",
       "[5 rows x 22555 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adataX = pd.DataFrame(adata.X.toarray(),index=adata.obs.index,columns=adata.var.index)\n",
    "adataX.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "      <th>ENSG00000001460.18</th>\n",
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       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
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       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 22555 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "index               ENSG00000001460.18  ENSG00000001461.17  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000010072.16  ENSG00000009780.15  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000048707.15  ENSG00000059588.10  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 1.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000041988.15  ENSG00000049245.13  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 2.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000052723.11  ENSG00000058799.15        ...          \\\n",
       "index                                                             ...           \n",
       "AAACCTGAGCGATTCT-0                 1.0                 0.0        ...           \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0        ...           \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0        ...           \n",
       "\n",
       "index               ENSG00000161835.11  ENSG00000173809.18  ENSG00000237126.8  \\\n",
       "index                                                                           \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0                0.0   \n",
       "\n",
       "index               ENSG00000236699.9  ENSG00000242252.2  ENSG00000242461.1  \\\n",
       "index                                                                         \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                0.0   \n",
       "\n",
       "index               ENSG00000231364.3  ENSG00000288023.1  ENSG00000211445.12  \\\n",
       "index                                                                          \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                 0.0   \n",
       "\n",
       "index               ENSG00000267547.1  \n",
       "index                                  \n",
       "AAACCTGAGCGATTCT-0                0.0  \n",
       "AAACCTGAGCTTTGGT-0                0.0  \n",
       "AAACCTGAGGCCCTCA-0                0.0  \n",
       "AAACCTGAGTAGCCGA-0                0.0  \n",
       "AAACCTGGTAGCGCTC-0                0.0  \n",
       "\n",
       "[5 rows x 22555 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adataSp = pd.DataFrame(adata.layers['spliced'].toarray(),index=adata.obs.index,columns=adata.var.index)\n",
    "adataSp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>index</th>\n",
       "      <th>ENSG00000001460.18</th>\n",
       "      <th>ENSG00000001461.17</th>\n",
       "      <th>ENSG00000010072.16</th>\n",
       "      <th>ENSG00000009780.15</th>\n",
       "      <th>ENSG00000048707.15</th>\n",
       "      <th>ENSG00000059588.10</th>\n",
       "      <th>ENSG00000041988.15</th>\n",
       "      <th>ENSG00000049245.13</th>\n",
       "      <th>ENSG00000052723.11</th>\n",
       "      <th>ENSG00000058799.15</th>\n",
       "      <th>...</th>\n",
       "      <th>ENSG00000161835.11</th>\n",
       "      <th>ENSG00000173809.18</th>\n",
       "      <th>ENSG00000237126.8</th>\n",
       "      <th>ENSG00000236699.9</th>\n",
       "      <th>ENSG00000242252.2</th>\n",
       "      <th>ENSG00000242461.1</th>\n",
       "      <th>ENSG00000231364.3</th>\n",
       "      <th>ENSG00000288023.1</th>\n",
       "      <th>ENSG00000211445.12</th>\n",
       "      <th>ENSG00000267547.1</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCGATTCT-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 22555 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "index               ENSG00000001460.18  ENSG00000001461.17  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000010072.16  ENSG00000009780.15  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000048707.15  ENSG00000059588.10  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 1.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000041988.15  ENSG00000049245.13  \\\n",
       "index                                                        \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 2.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0   \n",
       "\n",
       "index               ENSG00000052723.11  ENSG00000058799.15        ...          \\\n",
       "index                                                             ...           \n",
       "AAACCTGAGCGATTCT-0                 1.0                 0.0        ...           \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0        ...           \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0        ...           \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0        ...           \n",
       "\n",
       "index               ENSG00000161835.11  ENSG00000173809.18  ENSG00000237126.8  \\\n",
       "index                                                                           \n",
       "AAACCTGAGCGATTCT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                 0.0                 0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                 0.0                 0.0                0.0   \n",
       "\n",
       "index               ENSG00000236699.9  ENSG00000242252.2  ENSG00000242461.1  \\\n",
       "index                                                                         \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                0.0   \n",
       "\n",
       "index               ENSG00000231364.3  ENSG00000288023.1  ENSG00000211445.12  \\\n",
       "index                                                                          \n",
       "AAACCTGAGCGATTCT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGCTTTGGT-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGGCCCTCA-0                0.0                0.0                 0.0   \n",
       "AAACCTGAGTAGCCGA-0                0.0                0.0                 0.0   \n",
       "AAACCTGGTAGCGCTC-0                0.0                0.0                 0.0   \n",
       "\n",
       "index               ENSG00000267547.1  \n",
       "index                                  \n",
       "AAACCTGAGCGATTCT-0                0.0  \n",
       "AAACCTGAGCTTTGGT-0                0.0  \n",
       "AAACCTGAGGCCCTCA-0                0.0  \n",
       "AAACCTGAGTAGCCGA-0                0.0  \n",
       "AAACCTGGTAGCGCTC-0                0.0  \n",
       "\n",
       "[5 rows x 22555 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adataUsp = pd.DataFrame(adata.layers['spliced'].toarray(),index=adata.obs.index,columns=adata.var.index)\n",
    "adataUsp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n_cells</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ENSG00000001460.18</th>\n",
       "      <td>7252.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000001461.17</th>\n",
       "      <td>31838.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000010072.16</th>\n",
       "      <td>22712.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000009780.15</th>\n",
       "      <td>15246.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000048707.15</th>\n",
       "      <td>11175.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
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      ],
      "text/plain": [
       "                    n_cells\n",
       "index                      \n",
       "ENSG00000001460.18   7252.0\n",
       "ENSG00000001461.17  31838.0\n",
       "ENSG00000010072.16  22712.0\n",
       "ENSG00000009780.15  15246.0\n",
       "ENSG00000048707.15  11175.0"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.var.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>folder</th>\n",
       "      <th>n_genes</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>index</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCGATTCT-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2596</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGCTTTGGT-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>329</td>\n",
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       "    <tr>\n",
       "      <th>AAACCTGAGGCCCTCA-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>2178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGTAGCCGA-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGGTAGCGCTC-0</th>\n",
       "      <td>S4_L007</td>\n",
       "      <td>420</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                     folder  n_genes\n",
       "index                               \n",
       "AAACCTGAGCGATTCT-0  S4_L007     2596\n",
       "AAACCTGAGCTTTGGT-0  S4_L007      329\n",
       "AAACCTGAGGCCCTCA-0  S4_L007     2178\n",
       "AAACCTGAGTAGCCGA-0  S4_L007      253\n",
       "AAACCTGGTAGCGCTC-0  S4_L007      420"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Sequence of cleaning the adata:\n",
    "    1. Add data, spliced and unspliced,\n",
    "    2. Remove redundant columns\n",
    "    3. Recompute obs and var"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "d = {}\n",
    "drops = []\n",
    "for i,x in enumerate(adata.obs.index):\n",
    "    if x[:16] not in d:\n",
    "        d[x[:16]] = i\n",
    "    else:\n",
    "        j = d[x[:16]]\n",
    "        adataX.iloc[j,:] += adataX.iloc[j,:]\n",
    "        adataSp.iloc[j,:] += adataSp.iloc[j,:] \n",
    "        adataUsp.iloc[j,:] += adataUsp.iloc[j,:] \n",
    "        drops.append(x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "adataX.drop(index=drops,inplace=True)\n",
    "adataSp.drop(index=drops,inplace=True)\n",
    "adataUsp.drop(index=drops,inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "del d\n",
    "del drops"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "adataX = scp.sparse.csr_matrix(adataX.values)\n",
    "adataSp = scp.sparse.csr_matrix(adataSp.values)\n",
    "adataUsp = scp.sparse.csr_matrix(adataUsp.values)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "adat = ad.AnnData(X=adataX)\n",
    "adat.layers['spliced'] = adataSp\n",
    "adat.layers['unspliced'] = adataUsp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 33209 × 22555 \n",
       "    layers: 'spliced', 'unspliced'"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 33189 × 19804 \n",
       "    obs: 'n_genes'\n",
       "    var: 'n_cells'\n",
       "    layers: 'spliced', 'unspliced'"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sc.pp.filter_cells(adat,min_genes=200)\n",
    "sc.pp.filter_genes(adat,min_cells=3)\n",
    "adat"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>n_genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2592</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2177</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>420</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   n_genes\n",
       "0     2592\n",
       "1      328\n",
       "2     2177\n",
       "3      253\n",
       "4      420"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adat.obs.head()"
   ]
  }
 ],
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